More than a third of indigenous defendants held in custody awaiting trial or sentence will not go on to receive a jail sentence.

A routine late-night check revealed the trio wasn't in their rooms, a spokeswoman for the Department of Justice and Attorney-General says.

The correctional centre, 12 kilometres west of Townsville, has an adjoining 660-hectare farm that grows fruit and vegetables for inmates and a eucalyptus plantation that supplies gum leaves to an animal sanctuary.

The men may have been working on the plantation earlier in the day.

Police Minister Bill Byrne said while the trio didn't pose any perceived threat to the community, their escape was unacceptable and would be investigated.

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"This is a performance problem and one we need to get to the bottom of," he said.

Mr Byrne also said one of the escapees was due to be released in a "very short time".

"It defies logic," he said.

Jackson is serving six years and eight months for unlawful use of a motor vehicle, while Cobbo is serving five years eight months and Allen 10 months respectively for breaking and entering.